Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation

John R. Garbe, Christine G. Elsik, Eric Antoniou, James M. Reecy, Karl J Clark, Anand Venkatraman, Jae Woo Kim, Robert D. Schnabel, C. Michael Dickens, Russell D. Wolfinger, Scott C. Fahrenkrug, Jeremy F. Taylor

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72 of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76 of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.

Original languageEnglish (US)
Article number453638
JournalJournal of Biomedicine and Biotechnology
Volume2010
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Molecular Sequence Annotation
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Swine
Genes
Proteins
Genome
Gene expression
Gene Expression
Oligonucleotide Probes
Expressed Sequence Tags
Vertebrates
Sensitivity and Specificity

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Medicine
  • Genetics
  • Molecular Biology
  • Health, Toxicology and Mutagenesis
  • Medicine(all)

Cite this

Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation. / Garbe, John R.; Elsik, Christine G.; Antoniou, Eric; Reecy, James M.; Clark, Karl J; Venkatraman, Anand; Kim, Jae Woo; Schnabel, Robert D.; Michael Dickens, C.; Wolfinger, Russell D.; Fahrenkrug, Scott C.; Taylor, Jeremy F.

In: Journal of Biomedicine and Biotechnology, Vol. 2010, 453638, 2010.

Research output: Contribution to journalArticle

Garbe, JR, Elsik, CG, Antoniou, E, Reecy, JM, Clark, KJ, Venkatraman, A, Kim, JW, Schnabel, RD, Michael Dickens, C, Wolfinger, RD, Fahrenkrug, SC & Taylor, JF 2010, 'Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation', Journal of Biomedicine and Biotechnology, vol. 2010, 453638. https://doi.org/10.1155/2010/453638
Garbe, John R. ; Elsik, Christine G. ; Antoniou, Eric ; Reecy, James M. ; Clark, Karl J ; Venkatraman, Anand ; Kim, Jae Woo ; Schnabel, Robert D. ; Michael Dickens, C. ; Wolfinger, Russell D. ; Fahrenkrug, Scott C. ; Taylor, Jeremy F. / Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation. In: Journal of Biomedicine and Biotechnology. 2010 ; Vol. 2010.
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